Coleochaete appears in nature as microscopic filamentous plants that produce zoospores and oogametes, and as thick-walled resting cysts that are either associated with the vegetative filaments or are free in sediments.

Individual vegetative cells of Coleochaete species are usually 5-20 Ám in diameter and 1-4 times as long as broad, with a conspicuous cell wall. The cells contain a single plastid that occupies most of the cell periphery and contains at least one pyrenoid. The cells are organized into branched filaments that, together, produce a plant body less than 2 mm in diameter. This plant body is prostrate on, or embedded in, the substrate, with no plastid-bearing "erect" filaments extending from the substrate plane. In some species, the filaments are laterally compressed, forming a circular thallus with no apparent gaps between cells. Cultured plants that do not become fixed to a substrate may form spherical balls of cells.

Under certain conditions, especially when available nitrogen is in short supply, certain Coleochaete cells produce long colorless projections with a sheathed base ("sheathed setae"; image from University of Wisconsin). The seta-bearing cells are generally smaller and rounder than other vegetative cells, and the plastid in these cells undergoes a slow circular motion ("cyclosis").

Zoospores and male gametes are formed singly in "zoosporangia" and "antheridia", respectively. They are motile by means of two flagella of equal length inserted near but not at the apical end of the cell. Male gametes tend to be almost colorless, unlike the pigmented zoospores. Zoosporangia and antheridia look like vegetative cells until the motile cells are released.

Eggs ("oogonia") look like vegetative cells, although in some species an elongated receptive surface ("trichogyne") appears on the mature egg. They remain on the plant body until after fertilization and cyst maturation.

Cysts are spherical, are somewhat larger than vegetative cells and have a thickened wall with various types of ornamentation. They are formed from fertilized eggs. A more or less well organized jacket of sterile vegetative cells surrounds the cyst while it is attached to the plant body. The sterile cells are considered homologous with the archegonium, the sterile jacket of cells that surrounds the egg and embryo in all land plants.

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